X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;fp=rarefactsharedcommand.cpp;h=324f02852189c175ec7383d44a4e498fa4ccc7d5;hb=4a2d841cb97fb02351022efe9d7068b1dc212bf9;hp=357bc8708289e37063d731315b7411c715a05f1a;hpb=5a86e9e5a5a9e061e17b3ae64fb8881f14e53b8a;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 357bc87..324f028 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -84,7 +84,7 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
 			globaldata->Groups = Groups;
 			
 			string temp;
-			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "0.10"; }
+			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
 			convert(temp, freq); 
 			
 			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
@@ -133,7 +133,7 @@ void RareFactSharedCommand::help(){
 		m->mothurOut("The rarefaction.shared command parameters are label, iters, groups, jumble and calc.  No parameters are required.\n");
 		m->mothurOut("The rarefaction command should be in the following format: \n");
 		m->mothurOut("rarefaction.shared(label=yourLabel, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n");
-		m->mothurOut("The freq parameter is used indicate when to output your data.  It is a percentage of the number of sequences.  By default it is set to 0.10, meaning 10%. \n");
+		m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
 		m->mothurOut("Example rarefaction.shared(label=unique-0.01-0.03,  iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n");
 		m->mothurOut("The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness.\n");
 		m->mothurOut("The default value for groups is all the groups in your groupfile, and jumble is true.\n");